Noncoding RNA and protein coding gene co expression

Question

[gulamaltab]

I’m working with non coding rna to see their expression with ageing, i did differential analysis using deseq2 and got the ncRNA and protein coding genes, now I wanted to see the coexpression of ncRNA with coding genes, how do I do that? I’m new to bioinformatics so finding it really difficult, any help will be really appreciated. Thank you

[GouthamAtla]

What organism and what tissue ? How many samples do you have ?

Answer 1

[Kevin Blighe]

Just create a co-expression network using both coding and non-coding genes, and then explore the relationships between these via, for example, community structure: Network plot from expression data in R using igraph

Alernatively, if you use WGCNA, you can explore the relationships based on membership to particular modules.

A 'co-expression' network, remember, is just a way to summarise correlations between your variables or samples. Network analysis has fans and has enemies. I am yet to see how it has shaped hypotheses / conclusions in any major way.

A good read for you, recommended by an Italian colleague of mine: Gene co-expression analysis for functional classification and gene-disease predictions.

Kevin